Schema for TransposonPSI - Transposons Fragments Identified by TransposonPSI

JavaScript is disabled in your web browser

You must have JavaScript enabled in your web browser to use the Genome Browser

Schema for TransposonPSI - Transposons Fragments Identified by TransposonPSI

Database: DmojImproved Primary Table: transposon_psi Row Count: 7,180

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	improved_6498	`varchar(255)`	values
`chromStart`	1685	`int(10) unsigned`	range
`chromEnd`	3907	`int(10) unsigned`	range
`name`	TPSI_LINE_0	`varchar(255)`	values
`score`	825	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	1685	`int(10) unsigned`	range
`thickEnd`	3907	`int(10) unsigned`	range
`reserved`	200	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	1430,785	`longblob`
`chromStarts`	0,1436	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved	blockCount	blockSizes	chromStarts
585	improved_6498	1685	3907	TPSI_LINE_0	825	+	1685	3907	200	2	1430,785	0,1436
585	improved_6498	6535	8721	TPSI_LINE_1	745	+	6535	8721	200	2	1295,866	0,1319
585	improved_6498	11524	13569	TPSI_LINE_2	747	+	11524	13569	200	3	1295,368,287	0,1319,1757
585	improved_6498	16247	17492	TPSI_LINE_3	714	+	16247	17492	200	1	1244	0
585	improved_6498	51033	51192	TPSI_mariner_4	128	-	51033	51192	32768	1	158	0
585	improved_6498	58145	58856	TPSI_LINE_5	434	-	58145	58856	200	1	710	0
585	improved_6498	63599	65051	TPSI_LINE_6	665	-	63599	65051	200	1	1451	0
585	improved_6498	69464	71603	TPSI_TY1_Copia_7	995	-	69464	71603	8388608	3	1283,221,215	0,1283,1923
585	improved_6498	71610	72006	TPSI_gypsy_8	160	-	71610	72006	128	1	395	0
585	improved_6498	72032	73544	TPSI_TY1_Copia_9	371	-	72032	73544	8388608	1	1511	0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

TransposonPSI (transposon_psi) Track Description


	Description The D. mojavensis genome is searched against transposons open reading frames (ORF) profiles using TransposonPSI. The types of transposons in the library include ORFs from gypsy and copia polyproteins, cryptons, helitrons, DNA transposons, and LINE retrotransposons. The best chain per locus is shown in this evidence track. Methods TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. PSI-Blast is used with a collection of (retro-)transposon ORF homology profiles to identify statistically significant alignments. This method can be used to identify potential transposon ORFs within a protein set, or to identify regions of transposon homology within a larger genome sequence. References The TransposonPSI application is available for download at SourceForge.